CutSPR – Construction of Mutagenesis Vector based on the pJoe8999 plasmid system

CutSPR

:: DESCRIPTION

CutSPR is a bioinformatic tool for rapid primer design, and facilitates the cloning of specific CRISPR-Cas9-based mutagenesis plasmids.

::DEVELOPER

Göttingen Genomics Laboratory, Institut für Mikrobiologie and Genetik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOs
  • Python

:: DOWNLOAD

CutSPR

:: MORE INFORMATION

Citation

Schilling T, Dietrich S, Hoppert M, Hertel R.
A CRISPR-Cas9-Based Toolkit for Fast and Precise In Vivo Genetic Engineering of Bacillus subtilis Phages.
Viruses. 2018 May 4;10(5):241. doi: 10.3390/v10050241. PMID: 29734705; PMCID: PMC5977234.

plotIBD 20111108 – Plotting Sampled Inheritance Vectors in Pedigrees

plotIBD 20111108

:: DESCRIPTION

plotIBD is a perl script to assist with plotting sampled inheritance vectors in pedigrees

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 plotIBD

:: MORE INFORMATION

Citation:

Hum Hered. 2011;72(4):289-97. doi: 10.1159/000334083. Epub 2011 Dec 23.
Estimation and visualization of identity-by-descent within pedigrees simplifies interpretation of complex trait analysis.
Marchani EE1, Wijsman EM.

GEN3VA – Gene Expression and Enrichment Vector Analyzer

GEN3VA

:: DESCRIPTION

GEN3VA is a web-based system that enables the integrative analysis of aggregated collections of tagged gene expression signatures identified and extracted from GEO.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

GEN3VA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Nov 15;17(1):461.
GEN3VA: aggregation and analysis of gene expression signatures from related studies.
Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma’ayan A

jEcho 1.0C – An Evolved Weight Vector to CHaracterize the protein’s post-translational Modification mOtifs

jEcho 1.0C

:: DESCRIPTION

jEcho is an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.

::DEVELOPER

Health Informatics Lab (HILab)

:: SCREENSHOTS

jEcho

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • Java

:: DOWNLOAD

 jEcho

:: MORE INFORMATION

Citation

Interdiscip Sci. 2015 Jun;7(2):194-9. doi: 10.1007/s12539-015-0260-2. Epub 2015 Aug 6.
jEcho: an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.
Zhao M, Zhang Z, Mai G, Luo Y, Zhou F.

StarPrimer D’Signer 3.0.0.3 – Design of Primers for ENTRY Cloning to Create Donor Vector

StarPrimer D’Signer 3.0.0.3

:: DESCRIPTION

StarPrimer D′Signer is a software to facilitate the design of primers for the ENTRY cloning step to create the Donor Vector. The software is also very well suited for the design of primers in combination with a site-directed mutation approach. In this case it is used to design primers for introducing mutations into your gene of interest which then is transferred into a StarGate ENTRY vector to create a Donor Vector carrying the mutated gene of interest.

::DEVELOPER

IBA GmbH

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX
  • Microsoft Silverlight

:: DOWNLOAD

StarPrimer D’Signer

:: MORE INFORMATION

Figaro 1.05 – Novel Vector Trimming software

Figaro 1.05

:: DESCRIPTION

Figaro is a software tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence. By statistically modeling short oligonucleotide frequencies within a set of reads, Figaro is able to determine which DNA words are most likely associated with vector sequence.

::DEVELOPER

Figaro Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Figaro

:: MORE INFORMATION

Citation:

James Robert White, Michael Roberts, James A. Yorke and Mihai Pop
Figaro: a novel statistical method for vector sequence removal
Bioinformatics (2008) 24 (4): 462-467.